Buggy code:
public class MD5DB { private static final int MAX_RECORDS_TO_READ = 10000 ; public static final String LOCAL_MD5_DB_DIR = "integrationtests" ; public static final String GLOBAL_MD5_DB_DIR = "//humgen//gsa-hpprojects//GATK//data//integrationtests" ; protected static void ensureMd5DbDirectory ( ) { } public static String getMD5FilePath ( final String md5 , final String valueIfNotFound ) { } private static File getFileForMD5 ( final String md5 , final String dbPath ) { } private static void updateMD5Db ( final String md5 , final File resultsFile ) { } private static void copyFileToDB ( File dbFile , final File resultsFile ) { } private static byte [ ] getBytesFromFile ( File file ) throws IOException { } public static String assertMatchingMD5 ( final String name , final File resultsFile , final String expectedMD5 , final boolean parameterize ) { } public static String testFileMD5 ( final String name , final File resultsFile , final String expectedMD5 , final boolean parameterize ) { try { byte [ ] bytesOfMessage = MD5DB . getBytesFromFile ( resultsFile ) ; byte [ ] thedigest = MessageDigest . getInstance ( "MD5" ) . digest ( bytesOfMessage ) ; BigInteger bigInt = new BigInteger ( 1 , thedigest ) ; String filemd5sum = bigInt . toString ( 16 ) ; while ( ( filemd5sum . length ( ) ) < 32 ) filemd5sum = "0" + filemd5sum ; MD5DB . updateMD5Db ( filemd5sum , resultsFile ) ; if ( parameterize || ( expectedMD5 . equals ( "" ) ) ) { System . out . println ( String . format ( "PARAMETERIZATION[%s]:<seq2seq4repair_space>file<seq2seq4repair_space>%s<seq2seq4repair_space>has<seq2seq4repair_space>md5<seq2seq4repair_space>=<seq2seq4repair_space>%s,<seq2seq4repair_space>stated<seq2seq4repair_space>expectation<seq2seq4repair_space>is<seq2seq4repair_space>%s,<seq2seq4repair_space>equal?<seq2seq4repair_space>=<seq2seq4repair_space>%b" , name , resultsFile , filemd5sum , expectedMD5 , filemd5sum . equals ( expectedMD5 ) ) ) ; } else { System . out . println ( String . format ( "Checking<seq2seq4repair_space>MD5<seq2seq4repair_space>for<seq2seq4repair_space>%s<seq2seq4repair_space>[calculated=%s,<seq2seq4repair_space>expected=%s]" , resultsFile , filemd5sum , expectedMD5 ) ) ; System . out . flush ( ) ; if ( ! ( expectedMD5 . equals ( filemd5sum ) ) ) { <START_BUG> System . out . printf ( "#####<seq2seq4repair_space>Test<seq2seq4repair_space>%s<seq2seq4repair_space>is<seq2seq4repair_space>going<seq2seq4repair_space>fail<seq2seq4repair_space>#####%n" , name ) ; <END_BUG> String pathToExpectedMD5File = MD5DB . getMD5FilePath ( expectedMD5 , "[No<seq2seq4repair_space>DB<seq2seq4repair_space>file<seq2seq4repair_space>found]" ) ; String pathToFileMD5File = MD5DB . getMD5FilePath ( filemd5sum , "[No<seq2seq4repair_space>DB<seq2seq4repair_space>file<seq2seq4repair_space>found]" ) ; System . out . printf ( "#####<seq2seq4repair_space>Path<seq2seq4repair_space>to<seq2seq4repair_space>expected<seq2seq4repair_space>file<seq2seq4repair_space>(MD5=%s):<seq2seq4repair_space>%s%n" , expectedMD5 , pathToExpectedMD5File ) ; System . out . printf ( "#####<seq2seq4repair_space>Path<seq2seq4repair_space>to<seq2seq4repair_space>calculated<seq2seq4repair_space>file<seq2seq4repair_space>(MD5=%s):<seq2seq4repair_space>%s%n" , filemd5sum , pathToFileMD5File ) ; System . out . printf ( "#####<seq2seq4repair_space>Diff<seq2seq4repair_space>command:<seq2seq4repair_space>diff<seq2seq4repair_space>%s<seq2seq4repair_space>%s%n" , pathToExpectedMD5File , pathToFileMD5File ) ; DiffEngine . SummaryReportParams params = new DiffEngine . SummaryReportParams ( System . out , 20 , 10 , 0 ) ; boolean success = DiffEngine . simpleDiffFiles ( new File ( pathToExpectedMD5File ) , new File ( pathToFileMD5File ) , MD5DB . MAX_RECORDS_TO_READ , params ) ; if ( success ) System . out . printf ( "Note<seq2seq4repair_space>that<seq2seq4repair_space>the<seq2seq4repair_space>above<seq2seq4repair_space>list<seq2seq4repair_space>is<seq2seq4repair_space>not<seq2seq4repair_space>comprehensive.<seq2seq4repair_space>At<seq2seq4repair_space>most<seq2seq4repair_space>20<seq2seq4repair_space>lines<seq2seq4repair_space>of<seq2seq4repair_space>output,<seq2seq4repair_space>and<seq2seq4repair_space>10<seq2seq4repair_space>specific<seq2seq4repair_space>differences<seq2seq4repair_space>will<seq2seq4repair_space>be<seq2seq4repair_space>listed.<seq2seq4repair_space>Please<seq2seq4repair_space>use<seq2seq4repair_space>-T<seq2seq4repair_space>DiffObjects<seq2seq4repair_space>-R<seq2seq4repair_space>public//testdata//exampleFASTA.fasta<seq2seq4repair_space>-m<seq2seq4repair_space>%s<seq2seq4repair_space>-t<seq2seq4repair_space>%s<seq2seq4repair_space>to<seq2seq4repair_space>explore<seq2seq4repair_space>the<seq2seq4repair_space>differences<seq2seq4repair_space>more<seq2seq4repair_space>freely%n" , pathToExpectedMD5File , pathToFileMD5File ) ; } } return filemd5sum ; } catch ( Exception e ) { throw new RuntimeException ( ( "Failed<seq2seq4repair_space>to<seq2seq4repair_space>read<seq2seq4repair_space>bytes<seq2seq4repair_space>from<seq2seq4repair_space>calls<seq2seq4repair_space>file:<seq2seq4repair_space>" + resultsFile ) , e ) ; } } }

Fix:
System . out . printf ( "#####<seq2seq4repair_space>Test<seq2seq4repair_space>%s<seq2seq4repair_space>is<seq2seq4repair_space>going<seq2seq4repair_space>to<seq2seq4repair_space>fail<seq2seq4repair_space>#####%n" , name ) ;